Ultra-Perfect Sorting Scenarios

  • Aïda Ouangraoua
  • Anne Bergeron
  • Krister M. Swenson
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6398)

Abstract

Perfection has been used as a criteria to select rearrangement scenarios since 2004. However, there is a fundamental bias towards extant species in the original definition: ancestral species are not bound to perfection. Here we develop a new theory of perfection that takes an egalitarian view of species, and apply it to the complex evolution of mammal chromosome X.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Bérard, S., Bergeron, A., Chauve, C.: Conservation of combinatorial structures in evolution scenarios. In: Lagergren, J. (ed.) RECOMB-WS 2004. LNCS (LNBI), vol. 3388, pp. 1–14. Springer, Heidelberg (2005)CrossRefGoogle Scholar
  2. 2.
    Bérard, S., Bergeron, A., Chauve, C., Paul, C.: Perfect sorting by reversals is not always difficult. IEEE/ACM Trans. Comput. Biology Bioinform. 4(1), 4–16 (2007)CrossRefGoogle Scholar
  3. 3.
    Bérard, S., Chateau, A., Chauve, C., Paul, C., Tannier, E.: Perfect DCJ rearrangement. In: Nelson, C.E., Vialette, S. (eds.) RECOMB-CG 2008. LNCS (LNBI), vol. 5267, pp. 158–169. Springer, Heidelberg (2008)CrossRefGoogle Scholar
  4. 4.
    Bergeron, A., Chauve, C., de Montgolfier, F., Raffinot, M.: Computing Common Intervals of k Permutations, with Applications to Modular Decomposition of Graphs. In: Brodal, G.S., Leonardi, S. (eds.) ESA 2005. LNCS, vol. 3669, pp. 779–790. Springer, Heidelberg (2005)CrossRefGoogle Scholar
  5. 5.
    Bourque, G., Pevzner, P.A., Tesler, G.: Reconstructing the genomic architecture of ancestral mammals: Lessons from human, mouse, and rat genomes. Genome Research 14(4), 507–516 (2004)CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Braga, M.D., Gautier, C., Sagot, M.-F.: An asymmetric approach to preserve common intervals while sorting by reversals. Algorithms for Molecular Biology 4(16) (2009)Google Scholar
  7. 7.
    Figeac, M., Varré, J.-S.: Sorting by reversals with common intervals. In: Jonassen, I., Kim, J. (eds.) WABI 2004. LNCS (LNBI), vol. 3240, pp. 26–37. Springer, Heidelberg (2004)CrossRefGoogle Scholar
  8. 8.
    Heber, S., Stoye, J.: Finding all common intervals of k permutations. In: Amir, A., Landau, G.M. (eds.) CPM 2001. LNCS, vol. 2089, pp. 207–218. Springer, Heidelberg (2001)CrossRefGoogle Scholar
  9. 9.
    Hsu, W.-L.: PC-trees vs. PQ-trees. In: Wang, J. (ed.) COCOON 2001. LNCS, vol. 2108, pp. 207–217. Springer, Heidelberg (2001)CrossRefGoogle Scholar
  10. 10.
    Hsu, W.-L., McConnell, R.M.: PC trees and circular-ones arrangements. Theor. Comput. Sci. 296(1), 99–116 (2003)CrossRefGoogle Scholar
  11. 11.
    Landau, G.M., Parida, L., Weimann, O.: Using PQ trees for comparative genomics. In: Apostolico, A., Crochemore, M., Park, K. (eds.) CPM 2005. LNCS, vol. 3537, pp. 128–143. Springer, Heidelberg (2005)CrossRefGoogle Scholar
  12. 12.
    Sagot, M.-F., Tannier, E.: Perfect sorting by reversals. In: Wang, L. (ed.) COCOON 2005. LNCS, vol. 3595, pp. 42–51. Springer, Heidelberg (2005)CrossRefGoogle Scholar
  13. 13.
    Tesler, G.: GRIMM: genome rearrangements web server. Bioinformatics 18(3), 492–493 (2002)CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Aïda Ouangraoua
    • 1
  • Anne Bergeron
    • 2
  • Krister M. Swenson
    • 2
    • 3
  1. 1.INRIA LNE, LIFLUniversité Lille 1Villeneuve d’AscqFrance
  2. 2.LacimUniversité du Québec à MontréalMontréalCanada
  3. 3.Department of Mathematics and StatisticsUniversity of OttawaCanada

Personalised recommendations